Try forcing it to install the xt, or xtpe driver, i put some steps below if needed:
First download all drivers you will need. Do a clean uninstall of the drivers, by first uninstalling the drivers from the control panel. Install and update drivercleaner. Then restart in safe mode (Admin) and use drivercleaner. Then restart computer, make sure no internet connection. Then install the drivers, make it install the appropriate xt, or xtpe driver (this may, if there is some conflict, cause windows to become unusable, so proceed carefully, after all these mods are obviously not guaranteed to work). Afterwards, reboot and then check again the number of pipes.
I have the exact same card, pci-e (is your card BBA?), and tried to flash this (x800 pro 16p) bios (flashrom -f -p 0 newbios.bin, you're using the modified flasher right?), and my computer display would not appear. I had to flash blind back to my old bios (x800 pro 12p) before it would work. I haven't tried the x800xt or xtpe bioses yet.. I will though and report back. Did you have this same problem with the x800pro 16p bios?
Anyways, how did you find out what speed your x800 pro could handle (ie. you said your card could only do x800xt, not x800xt pe? I assume you might have overclocked it to the stock speeds of the x800xt, xtpe to see if it was stable.. If so what speeds did you check?
I will try to find out more on w1zzard's theory, technically we could find out by looking under the gpu heatsink to at least see whether there is a laser cut...=/